Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / Bioconductor/SummarizedExperiment issues and pull requests
#79 - Clarify withDimnames=FALSE in the documentation
Issue -
State: closed - Opened by SamGG 9 months ago
- 3 comments
#78 - add a section about interactive visualization
Pull Request -
State: closed - Opened by kevinrue 12 months ago
- 1 comment
#77 - Rows being removed from ASV table when building SummarizedExperiment
Issue -
State: closed - Opened by yasminhilliam about 1 year ago
#76 - Depreciated function calls in DelayedArray
Issue -
State: closed - Opened by mingl1997 about 1 year ago
- 4 comments
#75 - Warning and error message when using '$' operator on summarizedExperiment object
Issue -
State: closed - Opened by DijkJel over 1 year ago
- 5 comments
#74 - Warning about dim, nrow and ncol deprecated methods.
Issue -
State: open - Opened by charles-plessy over 1 year ago
#73 - colData Default in Constructor Inconsistency
Issue -
State: open - Opened by DarioS over 1 year ago
- 1 comment
#72 - metadata function is not exported as others
Issue -
State: closed - Opened by hsiaoyi0504 over 1 year ago
- 1 comment
#71 - Feature request: keep rownames(se) and rownames() of DataFrame nested in rowData(se) in sync
Issue -
State: closed - Opened by kevinrue over 1 year ago
- 4 comments
#70 - Curious about how Rd manuals are generated
Issue -
State: closed - Opened by mvfki over 1 year ago
- 3 comments
#69 - Add an `assaybind()` method
Issue -
State: open - Opened by multimeric over 1 year ago
#68 - package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'SummarizedExperiment'
Issue -
State: open - Opened by bakaufman over 1 year ago
- 1 comment
#67 - Erroneous behaviour when colData is data.frame
Issue -
State: open - Opened by TuomasBorman almost 2 years ago
#66 - `combineCols` should keep names in metadata with `use.names=TRUE`
Issue -
State: open - Opened by LTLA almost 2 years ago
#65 - Remove all dimnames in `combine_assays_by` to avoid constructor check failures
Issue -
State: closed - Opened by LTLA about 2 years ago
- 3 comments
#64 - `all.equal(x, y)` vs `all(x == y)`
Issue -
State: closed - Opened by LiNk-NY over 2 years ago
- 3 comments
#63 - Constructor could check that assay is in matric format
Issue -
State: closed - Opened by TuomasBorman over 2 years ago
- 2 comments
#62 - Consider assayData DataFrame for assays
Issue -
State: closed - Opened by jmw86069 over 2 years ago
- 6 comments
#61 - `combineCols()` and `combineRows()` not listed in 'Usage' section
Issue -
State: closed - Opened by PeteHaitch over 2 years ago
- 4 comments
#60 - Enforce unique assay names
Issue -
State: open - Opened by hpages over 2 years ago
- 2 comments
#59 - Should the show() method for SummarizedExperiment objects suggest saveHDF5SummarizedExperiment()?
Issue -
State: open - Opened by hpages almost 3 years ago
- 1 comment
Labels: enhancement
#58 - subset fails when subsetting a SummarizedExperiment object with no samples
Issue -
State: closed - Opened by kpagacz about 3 years ago
- 11 comments
#57 - Adding checkDimnames=FALSE to the SE constructor
Issue -
State: closed - Opened by LTLA about 3 years ago
- 1 comment
#56 - Constructor assigns wrong assay values to wrong samples and features
Issue -
State: closed - Opened by TuomasBorman about 3 years ago
- 7 comments
#55 - Subsetting
Issue -
State: closed - Opened by antagomir about 3 years ago
- 2 comments
#54 - add dims note
Pull Request -
State: closed - Opened by LiNk-NY about 3 years ago
- 1 comment
#53 - Add rownames check for cbind()
Issue -
State: open - Opened by tavareshugo about 3 years ago
#52 - Vignette Doesn't Specify Dimensionality Rules
Issue -
State: closed - Opened by DarioS about 3 years ago
- 1 comment
#51 - assay<- is too pedantic when the dimensions are named
Issue -
State: closed - Opened by LTLA about 3 years ago
- 2 comments
#50 - Add a showAsCell method for SummarizedExperiment objects
Issue -
State: closed - Opened by LTLA over 3 years ago
- 1 comment
#49 - Conversion to SingleCellExpriment object
Issue -
State: closed - Opened by zhli12 over 3 years ago
- 1 comment
#48 - Migrate SCE's flexible row combiner for general SE use.
Pull Request -
State: closed - Opened by LTLA over 3 years ago
- 10 comments
#47 - fail to create `rbind` for SE-derived class due to the validity check
Issue -
State: closed - Opened by fionarhuang over 3 years ago
- 2 comments
#46 - More informative error message for mismatching numbers of rows
Issue -
State: open - Opened by LTLA almost 4 years ago
#45 - Add utility to easily split rows/columns by a factor.
Pull Request -
State: closed - Opened by LTLA almost 4 years ago
- 1 comment
#44 - loading package taking too much memory
Issue -
State: open - Opened by spocks about 4 years ago
- 2 comments
#43 - Coercion from SummarizedExperiment to ExpressionSet creates an unlocked environment
Issue -
State: closed - Opened by tomsing1 about 4 years ago
- 3 comments
#42 - “SimpleAssays” is not a defined class
Issue -
State: closed - Opened by Georgy415 over 4 years ago
- 2 comments
#41 - Incorrect document page
Issue -
State: closed - Opened by Jiefei-Wang over 4 years ago
- 2 comments
#40 - Improving the performance when calling assays accessor on a SummarizedExperiment object?
Issue -
State: closed - Opened by Jiefei-Wang over 4 years ago
- 2 comments
#39 - Type conversion btw SimpleAssays and list
Pull Request -
State: closed - Opened by Jiefei-Wang over 4 years ago
- 2 comments
#38 - a = SimpleList(setNames(nm = list())); assays(SummarizedExperiment(a)) is no longer endomorphic
Issue -
State: closed - Opened by mtmorgan over 4 years ago
- 6 comments
#37 - error object 'normalize_names_replacement_value' not found
Issue -
State: closed - Opened by weibei43 over 4 years ago
- 9 comments
#36 - colData assignment should fail but does not
Issue -
State: open - Opened by vjcitn over 4 years ago
- 1 comment
#35 - colnames-related concerns
Issue -
State: closed - Opened by vjcitn over 4 years ago
- 5 comments
#34 - Resolve _R_CHECK_LENGTH_1_LOGIC2_ issue
Pull Request -
State: closed - Opened by LiNk-NY almost 5 years ago
- 2 comments
#33 - Slightly relaxing the rowData checks for cbind
Issue -
State: open - Opened by LTLA almost 5 years ago
#32 - Build an assay element to work from my own normalized count matrix
Issue -
State: closed - Opened by ramarquezo about 5 years ago
- 5 comments
#31 - Extraction isn't working with ShallowSimpleListAssays on Bioc Devel 3.10
Issue -
State: closed - Opened by mjsteinbaugh about 5 years ago
- 4 comments
#30 - Should `rowData` be merged with `mcols(gr)`?
Issue -
State: open - Opened by LiNk-NY about 5 years ago
- 2 comments
Labels: question
#29 - derived RSE to SE coercion discards names
Issue -
State: open - Opened by LTLA about 5 years ago
- 15 comments
#28 - seqinfo<-() fails when @rowData is a GRangesList
Issue -
State: closed - Opened by lawremi about 5 years ago
- 2 comments
#27 - c() does not work on SummarizedExperiment
Issue -
State: open - Opened by lawremi about 5 years ago
- 1 comment
#26 - SummarizedExperiment R package not allowing installation.
Issue -
State: closed - Opened by joao1980 about 5 years ago
- 8 comments
#25 - assayNames<- is reluctant to work
Issue -
State: closed - Opened by LTLA over 5 years ago
- 5 comments
#24 - Why is SummarizedExperiment graphic not directly included in package?
Issue -
State: closed - Opened by PeteHaitch over 5 years ago
- 4 comments
#23 - SummarizedExperiment::cbind
Issue -
State: open - Opened by tiagochst over 5 years ago
- 3 comments
#22 - Implement an all.equal() method for SummarizedExperiment objects that performs a "deep comparison"
Issue -
State: open - Opened by hpages over 5 years ago
#21 - Stop wrapping the user-supplied assays in a ref object when storing them in the "assays" slot of a SummarizedExperiment object
Issue -
State: closed - Opened by hpages over 5 years ago
- 1 comment
#20 - Convert ShallowSimpleListAssays into an S3 list
Issue -
State: closed - Opened by marcpaga over 5 years ago
- 3 comments
#19 - Allow clearing of colData
Issue -
State: closed - Opened by LTLA almost 6 years ago
- 1 comment
#18 - Added SE coercion advice to derivation vignette
Pull Request -
State: closed - Opened by LTLA almost 6 years ago
- 1 comment
#17 - SummarizedExperiment doesn't work with data.frame input
Issue -
State: closed - Opened by LTLA almost 6 years ago
- 4 comments
#16 - all.equal does not work for SE objects
Issue -
State: closed - Opened by LTLA almost 6 years ago
- 5 comments
#15 - Advised on implementation of SE coercion methods
Pull Request -
State: closed - Opened by LTLA almost 6 years ago
- 1 comment
#14 - Error in coercion SummarizedExperiment <-> ExpressionSet
Issue -
State: closed - Opened by lgeistlinger about 6 years ago
- 1 comment
#13 - rowData rownames issue explored at BioC2018
Issue -
State: open - Opened by mikelove about 6 years ago
- 6 comments
#12 - Use DelayedArray:::set_dimnames() in realize,SummarizedExperiment-method
Pull Request -
State: closed - Opened by PeteHaitch over 6 years ago
- 2 comments
#11 - Fix 'getter' example in 'Extensions' vignette
Pull Request -
State: closed - Opened by PeteHaitch over 6 years ago
- 1 comment
#10 - Detailed instructions for class extension
Pull Request -
State: closed - Opened by LTLA over 6 years ago
- 23 comments
#9 - Add BACKEND argument to realize,SummarizedExperiment-method
Pull Request -
State: closed - Opened by PeteHaitch over 6 years ago
#8 - SummarizedExperiment() constructor with SummarizedExperiment given as argument should return the same SummarizedExperiment
Issue -
State: closed - Opened by dvantwisk over 6 years ago
- 5 comments
#7 - Difficult bug when colnames are arrays
Issue -
State: closed - Opened by LTLA over 6 years ago
- 6 comments
#6 - addition of explicit subset method for SummarizedExperiment class
Pull Request -
State: closed - Opened by schifferl over 6 years ago
#5 - import / export as loom
Issue -
State: closed - Opened by mtmorgan over 6 years ago
- 1 comment
#4 - Fix broken link to SummarizedExperiment doc
Pull Request -
State: closed - Opened by LiNk-NY over 6 years ago
#3 - HDF5ArraySeed slot name 'filepath' instead of 'file'.
Pull Request -
State: closed - Opened by Liubuntu over 6 years ago
- 1 comment
#2 - rowData does not contain the rownames
Issue -
State: closed - Opened by LTLA almost 7 years ago
- 34 comments
#1 - More informative errors for assay() with names.
Pull Request -
State: closed - Opened by LTLA almost 7 years ago